Re: split channels and all files in a directory
Posted by
Carnë Draug on
Apr 07, 2011; 2:25pm
URL: http://imagej.273.s1.nabble.com/split-channels-and-all-files-in-a-directory-tp3685101p3685102.html
On 7 April 2011 15:04, Ramon Guirado <
[hidden email]> wrote:
> Hi, I'm trying to write a macro able to open all the files in a directory,
> split the channels of the images and analyze particles in this separated
> channels as well as the composite between some of them (they will be also
> binarized, etc...). I have just done small macros using the macro recorder,
> so I don't know how to do it, I'm trying to get the identity of every image
> in a directory and then I guess after the image calculator, I will have to
> identify the new windows just created so they are processed as well, and
> then do that recursively, but I feel a little bit lost... which would be the
> easiest way to proceed? by know I'll try to understand the macro posted
> by Carnë Draug..
>
> Thanks,
>
>
> ramon
I wrote a macro some time ago that does a similar thing. It opens all
images, makes them composite, use one channel to find the nucleus
(DAPI stained), and the two other channels to analyze particles inside
the nucleus. I wrote it as macro and regret it, it's terribly
confusing code. I find the ImageJ macro language terribly frustating.
I should have bothered to learn Python to do it. Anyway, I pasted it
into pastebin
http://pastebin.com/R5dPsyqMYou'll also need the other functions I posted before (I place them in
macros/Library.txt so I don't have to bother copying into every
macro).
Carnë